PrimerDesigner plugin for JBrowse Written by Nathan Liles (nml5566@gmail.com)
PrimerDesigner displays primers for a highlighted region's DNA sequence.
This plugin is very alpha.
Bio::PrimerDesigner is a perl module frontend for primer3. It can be installed via CPAN:
sudo cpan Bio::PrimerDesigner
This legacy requirement is due to Bio::PrimerDesigner, which currently isn't compatible with anything newer.
The older versions can be found here
*Note: if primer3 is installed anywhere other than the default $PATH, you'll need to change the BINPATH constant in PrimerDesigner/bin/primer-designer.pl to reflect that.
First copy the PrimerDesigner/ folder into your JBrowse plugins/ directory cp -r PrimerDesigner/ /your/jbrowse/path/plugins
Next, change permissions on a couple of paths so Apache can use them:
*Note: Make sure to substitute $APACHE_USER with the appropriate Apache user for your OS (www-data for Linux & _www for OSX)
cd /your/jbrowse/path/plugins/PrimerDesigner
sudo chmod 764 bin/primer-designer.pl
sudo chown $APACHE_USER bin/primer-designer.pl
sudo chmod 764 tmp
sudo chown $APACHE_USER tmp
Then, add the following to Apache's httpd.conf:
<Directory /your/jbrowse/path/plugins/PrimerDesigner/bin>
Options +ExecCGI
AddHandler cgi-script .pl
</Directory>
Make sure to reboot Apache after the change
Finally, edit JBrowse's jbrowse_conf.json and add PrimerDesigner to the plugin list: plugins: [ 'PrimerDesigner' ],
If everything has gone well, you should see a PrimerDesigner pulldown option in the menu